If you have to write a research paper you will always wish to have software that can help you in managing all the related literature, 
arrange all PDFs according to your names & tag, help you in citation, make the annotation easy and make it available to other devices whenever you need it. So here is a compact list of different Software/Plugins/Browsers add-Ons/Tools that can help you managing your research papers and make the citation work easy.
Mendeley:
Mendeley is one of the best, free and latest tools/software for managing research papers, citation and research. Exceptional features of Mendeley are 2GB space for web storage, Extraction of citation details from PDFs without embedded metadata, Mobile & iPad support & Free and open database approaching 100 million documents. Mendeley can be easily downloaded from their official website after creating an account. The comparison of mendeley is quite clear on the official site of mendeley with other such software.
See all the features in this video:
Zotero:
Collect, Manage, Organize, Cite & Sync different research papers and make your personal library and collection. Zotero is a Browser plugin that works with Mozilla, Google Chrome & Safari. It works best with Mozilla Firefox.
You can create and join research groups to focus on any topic your choice. Each group can share its own research library, notes, and discussion threads.
Docear:
Docear is another open-source literature management tool that can be handy for arranging and classifying a large data of research papers, journals & books.
Papers 3:
Papers 3 is Apple Design Award and Ars Design Award winning software for literature management. It’s not a freeware but it offers a special discount for students. A student can buy it in 34 Euro. The same company also offers a same tool for Windows with the name of Papers 1.3 with the same pricing.
Citavi:
Another knowledge managing tool that can make paper writing easy. Citavi is not a free software although it offers free license to students of different universities. You can also win Citavi for free with their lucky draw.
Endnote:
Endnote, the most powerful tool for your research, is famous and easy to use software for collection and managing of research papers, book and journals. The best thing about the endnote is that they offer a nice collection of tutorials for using their software. You can watch tutorial on their YouTube Channel easily and free of c0st.
Qiqqa:
Collecting and reading large number of papers, discovering new papers, PDF management, editing details of research papers, editing metadata of papers, importing library from other software i.e zotera & EndNote & Exporting library everything becomes easy with Qiqqa. Qiqqa also have OSR, Optical Character Recognition, that can read images too. Qiqqa is free and you can download it from their official website. Here is a comparison of Qiqqa with other literature managing software/tools.
RefWorks:
RefWorks is a powerful web-based service, providing for the integration of the newest technologies to support researchers with effective tools. Users can easily organize, access, and disseminate information within seconds — offering global portability to today’s modern researcher.
RefWorks allows you to:
- Create a personal database online
- Import information from other sources
- Share information
- Format bibliographies and manuscripts in seconds
RedCube:
RedCube promises you a never before experience for reading, managing and citation work for your research paper. RedCube has some great features like importing PDFs from your computer and making them full-text searchable, adding paper to RedCube directly from web, easy writing & citation and sync & backup options. It’s available free for Mac & Windows.
Colwiz:
Colwiz is another reference management, research collaboration and productivity software developed by the researcher of The Oxford University. It’s freeware and also offer tutorials. It’s for Windows, Mac & Android.
JabRef:
BibDesk:
KBibTeX:
